A visualization method and system for a molecular model and its vibration modes

Abstract

The present invention provides a method and a system for visualizing a molecular model and its vibration modes. Among them, step 1: Obtain a target calculation file; step 2: Extract the atomic positions of target atoms and lattice basis vectors according to the target calculation file; step 3: Extract the vibration frequencies of special points and the eigenvectors of target atoms according to the target calculation file; step 4: Draw a molecular model according to the atomic positions and lattice basis vectors; step 5: Extract the real part of the eigenvector and perform vector synthesis to determine the first vibration displacement of the target atom at different vibration frequencies; step 6: Based on the visualization rules, determine the visual output according to the molecular model and the first vibration displacement. The method and system for visualizing the molecular model and its vibration modes of the present invention draw the molecular model according to the atomic positions and lattice basis vectors, which is more accurate; the real part of the eigenvector is synthesized by vectors to determine the first vibration displacement, and the molecular model and the first vibration displacement are visually displayed, which is more user-friendly.

Description

Technical Field

[0001] The present invention relates to the technical field of chemoinformatics, and particularly relates to a method and system for visualizing a molecular model and its vibration modes. Background Art

[0002] At present, with the continuous improvement of computer computing power, first-principles calculation has gradually become an important means for studying the properties of materials in chemistry and materials engineering. By visualizing the molecular model, the structure and shape of the molecule can be intuitively understood. The vibration mode describes the vibration mode and frequency of the atoms in the molecule. By visualizing the vibration mode, the changes and interactions of the molecule during vibration can be understood. However, since the commonly used first-principles calculation software often requires the use of specialized computers and systems, and the calculated results are all data files, it is often impossible to directly display the calculated molecular model and results.

[0003] The invention patent with the application number: CN201910566848.3 discloses a method for finding the glass structure gene. The method includes: determining the atomic types for structure search according to the glass system; performing structure screening based on first principles to screen out the compounds that can be formed by the interaction between each of the atoms; comparing the formation energy and phonon spectrum of each of the compounds to obtain the compounds that can stably exist; constructing a glass structure composition diagram based on the compounds that can stably exist, and the microstructure unit of the glassy compound adjacent to the target glass composition point is the structure gene of the glass.

[0004] However, the phonon spectrum results on the material project calculation platform used in the prior art are single, and the structures targeted are often inaccurate. The calculated results are only redundant data, which is not conducive to the understanding of R & D personnel and is not user-friendly enough.

[0005] In view of this, there is an urgent need for a method and system for visualizing a molecular model and its vibration modes to at least solve the above deficiencies. Summary of the Invention

[0006] One of the purposes of the present invention is to provide a method for visualizing a molecular model and its vibration modes. According to the obtained target calculation file, the atomic positions of the target atoms in the molecular structure, the lattice basis vectors, the vibration frequencies of the special points in the molecular structure, and the eigenvectors corresponding to each target atom are extracted respectively. According to the atomic positions and lattice basis vectors, the molecular model is drawn, and the construction of the molecular model is more accurate; the real part of the eigenvector is introduced to perform vector synthesis to determine the first vibration displacement, and the molecular model and the first vibration displacement are visually displayed, which is more user-friendly.

[0007] A method for visualizing a molecular model and its vibration modes provided by an embodiment of the present invention includes:

[0008] Step 1: Obtain the target calculation file;

[0009] Step 2: According to the target calculation file, extract the atomic positions of the target atoms and the lattice basis vectors in the molecular structure;

[0010] Step 3: According to the target calculation file, extract the vibration frequencies of the special points in the molecular structure and the eigenvectors corresponding to each target atom;

[0011] Step 4: Draw the molecular model according to the atomic positions and the lattice basis vectors;

[0012] Step 5: Extract the real part of the eigenvector and perform vector synthesis to determine the first vibration displacement of each target atom at different vibration frequencies;

[0013] Step 6: Based on the preset visualization rules, determine the visualization output according to the molecular model and the first vibration displacement.

[0014] Preferably, Step 1: Obtain the target calculation file, including:

[0015] Obtain the data file of the first-principles calculation software;

[0016] Obtain the call script of the PWphonon module;

[0017] Determine the target calculation file according to the call script and the data file.

[0018] Preferably, Step 3: According to the target calculation file, extract the vibration frequencies of the special points in the molecular structure and the eigenvectors corresponding to each target atom, including:

[0019] Step 3.1: Create an empty array;

[0020] Step 3.2: Obtain the target pointer;

[0021] Step 3.3: Search for the target array through the target pointer;

[0022] Step 3.4: If the search is successful, determine the first frequency information of the specific wave vector of the target array and store the first frequency information in the corresponding empty array;

[0023] Step 3.5: If the determination of the first frequency information is successful, continue to search for the eigenvector and store the real part and the imaginary part of the eigenvector in the corresponding empty array;

[0024] Step 3.6: Loop through Steps 3.2 to 3.5 until the search result of the target pointer in Step 3.3 is not the target array.

[0025] Preferably, Step 4: Draw the molecular model according to the atomic positions and the lattice basis vectors, including:

[0026] Create a three-dimensional space;

[0027] Draw lattice boundary points and lattice frames according to lattice basis vectors;

[0028] Determine a three-dimensional crystal according to the lattice boundary points and lattice frames;

[0029] Obtain the element name of the target atom;

[0030] Construct a molecular model in the three-dimensional space according to the three-dimensional crystal and the element name.

[0031] Preferably, constructing a molecular model in the three-dimensional space according to the three-dimensional crystal and the element name includes:

[0032] Determine the first index keyword according to the element name;

[0033] Determine the second index keyword, atomic diameter, and color mapping scheme according to the periodic table of elements;

[0034] Perform keyword matching on the determined first index keyword and second index keyword;

[0035] If the matching is successful, use the atomic diameter corresponding to the second index keyword as the target diameter of the target atom corresponding to the first index keyword. At the same time, use the color mapping scheme corresponding to the second index keyword as the target color mapping scheme of the target atom;

[0036] Obtain the configuration template of the three-dimensional space;

[0037] Based on the configuration template, determine configuration parameters according to the target diameter and target color mapping scheme;

[0038] Configure the three-dimensional space according to the configuration parameters to obtain the molecular model constructed in the three-dimensional space.

[0039] Preferably, step 6: Based on preset visualization rules, determine the visualization output according to the molecular model and the first vibration displacement, including:

[0040] Obtain the view control instructions of the target person; the view control instructions include: elevation angle control instructions and azimuth angle control instructions;

[0041] Control the process output according to the view control instructions and obtain the visualization output after the control is completed.

[0042] A visualization method for a molecular model and its vibration mode provided by an embodiment of the present invention further includes:

[0043] Step 7: Determine the molecular vibration result according to the visualization output and perform corresponding analysis on the molecular vibration result;

[0044] Among them, step 7: Determine the molecular vibration results based on the visual output, and perform corresponding analysis on the molecular vibration results, including:

[0045] Obtain the molecular vibration analysis requirements of the visual output;

[0046] Analyze the molecular vibration analysis requirements to obtain multiple vibration analysis requirement items;

[0047] Construct a data extraction template according to the vibration analysis requirement items;

[0048] Based on big data, determine the first target big data according to the data extraction template;

[0049] Determine the analysis result according to the molecular vibration result and the first target big data.

[0050] Preferably, determining the analysis result according to the molecular vibration result and the first target big data includes:

[0051] Extract the second frequency information from the analysis result, and at the same time, extract the third frequency information of the first target big data;

[0052] Determine the frequency distribution according to the second frequency information and the third frequency information;

[0053] Analyze the frequency distribution to determine multiple frequency interpolations;

[0054] Cluster the frequency interpolations to obtain the target number of clustering sets;

[0055] Determine the average frequency interpolation of each clustering set;

[0056] Intercept the target frequency distribution according to the average frequency interpolation and the frequency distribution;

[0057] Obtain the second target big data according to the target frequency distribution;

[0058] Determine the analysis result according to the molecular vibration result and the second target big data;

[0059] Among them, obtaining the second target big data according to the target frequency distribution includes:

[0060] Determine the third frequency information corresponding to the target frequency distribution and use it as the fourth frequency information;

[0061] Obtain the first target big data corresponding to the fourth frequency information and use it as the second target big data.

[0062] Preferably, determining the analysis result according to the molecular vibration result and the second target big data includes:

[0063] Train a vibration demonstration model according to the second target big data;

[0064] Obtain the second vibration displacement demonstrated by the vibration demonstration model;

[0065] Compare the first vibration displacement with the second vibration displacement to determine whether there is a difference in patterns; the differences in patterns include: vibration period and vibration amplitude;

[0066] If there is a difference in patterns, obtain the demonstration model of the second vibration displacement;

[0067] Compare the molecular model with the demonstration model to determine the model differences; the model differences include: chemical bond parameters and field parameters;

[0068] Based on a preset analysis model, determine the analysis result corresponding to the model difference according to the chemical bond parameters and field parameters.

[0069] A visualization system for a molecular model and its vibration mode provided by an embodiment of the present invention includes:

[0070] A target calculation file acquisition subsystem for acquiring a target calculation file;

[0071] A first extraction subsystem for extracting the atomic positions and lattice basis vectors of target atoms in the molecular structure according to the target calculation file;

[0072] A second extraction subsystem for extracting the vibration frequencies of special points in the molecular structure and the eigenvectors corresponding to each target atom according to the target calculation file;

[0073] A molecular model drawing subsystem for drawing a molecular model according to the atomic positions and lattice basis vectors;

[0074] A vector synthesis subsystem for extracting the real part of the eigenvector and performing vector synthesis to determine the first vibration displacement of each target atom at different vibration frequencies;

[0075] A visualization output subsystem for determining the visualization output based on preset visualization rules according to the molecular model and the first vibration displacement.

[0076] The beneficial effects of the present invention are:

[0077] According to the obtained target calculation file, the present invention respectively extracts the atomic positions, lattice basis vectors, vibration frequencies of special points in the molecular structure, and the eigenvectors corresponding to each target atom in the molecular structure, draws a molecular model according to the atomic positions and lattice basis vectors, and the construction of the molecular model is more accurate; the real part of the eigenvector is introduced for vector synthesis to determine the first vibration displacement, and the molecular model and the first vibration displacement are visually displayed, which is more user-friendly.

[0078] Other features and advantages of the present invention will be set forth in the following description, and in part will be obvious from the description, or may be learned by practice of the present invention. The objectives and other advantages of the present invention may be realized and attained by the structure particularly pointed out in the written description, claims, as well as the drawings.

[0079] The technical solution of the present invention will be further described in detail below with reference to the drawings and embodiments. Description of the Drawings

[0080] The drawings are used to provide a further understanding of the present invention, and constitute a part of the description. Together with the embodiments of the present invention, they are used to explain the present invention, but do not constitute a limitation to the present invention. In the drawings:

[0081] Figure 1 It is a schematic diagram of a visualization method for a molecular model and its vibration mode in an embodiment of the present invention;

[0082] Figure 2 It is a schematic diagram of the visualization output in an embodiment of the present invention;

[0083] Figure 3 It is a schematic diagram of a visualization system for a molecular model and its vibration mode in an embodiment of the present invention. Detailed Embodiments

[0084] The following describes the preferred embodiments of the present invention with reference to the drawings. It should be understood that the preferred embodiments described herein are only for the purpose of illustrating and explaining the present invention, and are not intended to limit the present invention.

[0085] The embodiment of the present invention provides a visualization method for a molecular model and its vibration mode, as Figure 1 shown, including:

[0086] Step 1: Obtain a target calculation file; wherein, the target calculation file is a file obtained by the system through calculating and processing the data file of the first-principles calculation software;

[0087] Step 2: Extract the atomic positions and lattice basis vectors of target atoms in the molecular structure according to the target calculation file; wherein, the molecular structure is the molecular structure of the molecule to be visualized; the atomic position is the relative position of the target atom in the molecular structure; the lattice basis vector is the basic building block describing the crystal structure, and is used to represent the periodic repetition property of the lattice;

[0088] Step 3: Extract the vibration frequencies of special points of the molecular structure and the eigenvectors corresponding to each target atom according to the target calculation file; wherein, the special point is a specific wave vector; the eigenvector is a vector composed of the eigenvalues of the target atom, and the eigenvalue is, for example, a frequency value;

[0089] Step 4: Draw a molecular model based on the atomic positions and lattice basis vectors; wherein, the molecular model is: a three-dimensional model corresponding to the molecular structure;

[0090] Step 5: Extract the real part of the eigenvector and perform vector synthesis to determine the first vibration displacement of each target atom at different vibration frequencies; wherein, the eigenvector has a real part and an imaginary part; the real part represents the spatial distribution of the displacement of the vibration mode in space, which describes the actual displacement of the atom during vibration. A positive real part indicates that the atom deviates from the equilibrium position in a certain direction during vibration, while a negative real part indicates that the atom deviates from the equilibrium position in the opposite direction during vibration. The larger the real part, the greater the displacement; the imaginary part represents the phase information of the vibration mode, which describes the relative time delay of the vibration. The phase of the vibration mode refers to the offset of the periodic change of the atom during vibration relative to a reference point, and the imaginary part can be positive or negative; the real part and the imaginary part of the eigenvector jointly determine the shape and behavior of the vibration mode. However, the imaginary part data of the eigenvector is mainly reflected in the time dimension and has little reference value for the static diagram finally generated by the present invention, because one of the main data extracted by the present invention is the real part of the eigenvector; the first vibration displacement refers to the displacement or deviation of the atom from its equilibrium position or initial position during vibration;

[0091] Step 6: Based on the preset visualization rules, determine the visualization output according to the molecular model and the first vibration displacement. Wherein, the preset visualization rules are: use a three-dimensional visualization model to visually display the molecular model and the first vibration displacement; the visualization output is: a visualization image, such as Figure 2 shown.

[0092] The working principle and beneficial effects of the above technical solution are:

[0093] According to the obtained target calculation file, the present application respectively extracts the atomic positions of target atoms in the molecular structure, the lattice basis vectors, the vibration frequencies of special points in the molecular structure, and the eigenvectors corresponding to each target atom. Based on the atomic positions and lattice basis vectors, a molecular model is drawn, and the construction of the molecular model is more accurate; the real part of the eigenvector is introduced for vector synthesis to determine the first vibration displacement, and the molecular model and the first vibration displacement are visually displayed, which is more user-friendly.

[0094] In one embodiment, Step 1: Obtain a target calculation file, including:

[0095] Obtain the data file of the first-principles calculation software; wherein, the first-principles calculation software is: PWmat;

[0096] Obtain the calling script for the PWphonon module; where the PWphonon module is part of the PWmat software suite and is used to calculate the vibrational properties of solid materials within the framework of quantum mechanical density functional theory (DFT); the calling script is a calling program that contains the required atomic positions and lattice basis vectors. Before running the calling script, the system saves the data results obtained from the software module calculation in the script directory with the file name "band.yaml". When running the calling script, the program will open the band.yaml file in read-write mode and copy all the data in it to the variable data. band.yaml is an input file used to describe the phonon band calculation path;

[0097] Determine the target calculation file according to the calling script and the data file.

[0098] The working principle and beneficial effects of the above technical solution are as follows:

[0099] This application introduces the calling script of the PWphonon module to determine the target calculation file of the data file, improving the accuracy of the calculation.

[0100] In one embodiment, step 3: Extract the vibration frequencies of the special points of the molecular structure and the eigenvectors corresponding to each target atom according to the target calculation file, including:

[0101] Step 3.1: Create an empty array; where the empty array is used to store the elements found by the subsequent pointers;

[0102] Step 3.2: Obtain the target pointer; where the target pointer is: [0, 0, 0];

[0103] Step 3.3: Search for the target array through the target pointer; where the target array is: [0, 0, 0];

[0104] Step 3.4: If the search is successful, determine the first frequency information of the specific wave vector of the target array and store the first frequency information in the corresponding empty array; where the first frequency information is the frequency value of the specific wave vector;

[0105] Step 3.5: If the determination of the first frequency information is successful, continue to search for the eigenvector and store the real part and imaginary part of the eigenvector in the corresponding empty array; where the eigenvector refers to the eigenvector corresponding to the vibration mode of each atom. Phonon calculation can obtain the vibration frequencies and vibration modes at different wave vectors in the material, and each vibration mode corresponds to an eigenvector. The eigenvector describes the displacement direction and amplitude of the atom in the vibration mode. For each vibration mode, the eigenvector is a column vector whose dimension is equal to the number of atoms in the system, and each component represents the displacement of the corresponding atom in this vibration mode;

[0106] Step 3.6: Loop through Steps 3.2 to 3.5 until the search result of the target pointer in Step 3.3 is not the target array.

[0107] The working principle and beneficial effects of the above technical solution are as follows:

[0108] This application introduces the vibration frequency of the special point searched by the target pointer and the eigenvector of the target atom, and stores the frequency information and eigenvector in the corresponding arrays, improving the extraction efficiency of the vibration frequency and eigenvector.

[0109] In one embodiment, Step 4: Draw a molecular model based on the atomic positions and lattice basis vectors, including:

[0110] Create a three-dimensional space; where the three-dimensional space is the construction space of the molecular model;

[0111] Draw lattice boundary points and lattice frames according to the lattice basis vectors;

[0112] Determine a three-dimensional crystal based on the lattice boundary points and lattice frames; where the three-dimensional crystal is: a crystal structure with three spatial dimensions, also known as a stereoscopic crystal, composed of atoms, ions or molecules in a regular manner and having a periodic structure;

[0113] Obtain the element name of the target atom; where the element name is: the type of element, such as: sodium;

[0114] Construct a molecular model in the three-dimensional space based on the three-dimensional crystal and the element name.

[0115] The working principle and beneficial effects of the above technical solution are as follows:

[0116] This application draws lattice boundary points and lattice frames according to the lattice basis vectors, determines the completed three-dimensional crystal, and constructs a molecular model based on the element name and the three-dimensional crystal, improving the suitability of the construction of the molecular model.

[0117] In one embodiment, constructing a molecular model in the three-dimensional space based on the three-dimensional crystal and the element name includes:

[0118] Determine the first index keyword according to the element name; where the first index keyword is: the semantics corresponding to the element name;

[0119] Determine the second index keyword, atomic diameter, and color mapping scheme according to the periodic table of elements; where the second index keyword is: the semantics corresponding to the element in the periodic table of elements; the color mapping scheme is preset manually, specifically: which element is mapped to which color when constructing the molecular model;

[0120] Perform keyword matching on the determined first index keyword and second index keyword; where the keyword matching is: semantic matching;

[0121] If the matching is successful, use the atomic diameter corresponding to the second index keyword as the target diameter of the target atom corresponding to the first index keyword. Meanwhile, use the color mapping scheme corresponding to the second index keyword as the target color mapping scheme of the target atom.

[0122] Obtain the configuration template for the three-dimensional space; wherein, the configuration template restricts the configuration of only the parameters of the three-dimensional space.

[0123] Based on the configuration template, determine the configuration parameters according to the target diameter and the target color mapping scheme; wherein, the configuration parameters are: setting the input value of which input terminal of the three-dimensional space carrying platform.

[0124] Configure the three-dimensional space according to the configuration parameters to obtain the molecular model constructed by the three-dimensional space.

[0125] The working principle and beneficial effects of the above technical solution are as follows:

[0126] In this application, according to the element name, determine the first index keyword. Meanwhile, according to the periodic table of elements, determine the second index keyword, atomic diameter, and color mapping scheme. Match the first index keyword and the second index keyword to determine the matching target diameter and target color mapping scheme, improving the determination efficiency of the target diameter and target color mapping scheme. Based on the configuration template of the three-dimensional space, determine the configuration parameters according to the target diameter and the target color mapping scheme and perform corresponding configuration, making the process of molecular construction more standardized and standard.

[0127] In one embodiment, step 6: Based on the preset visualization rules, determine the visualization output according to the molecular model and the first vibration displacement, including:

[0128] Obtain the view control instruction of the target person; the view control instruction includes: elevation angle control instruction and azimuth angle control instruction; wherein, the target person is: the user of the visualization platform for the molecular model and its vibration mode; the elevation angle control instruction is: a computer instruction for controlling the change of the elevation angle of the molecular model; the azimuth angle control instruction is: a computer instruction for controlling the change of the azimuth angle of the molecular model.

[0129] According to the view control instruction, control the process output and obtain the visualization output after the control is completed. Wherein, the process output is: the three-dimensional model before outputting the final visualization output.

[0130] The working principle and beneficial effects of the above technical solution are as follows:

[0131] This application introduces a view control instruction to control the process output and complete the view control instruction, making the observation process of the target person more comprehensive.

[0132] An embodiment of the present invention provides a method for visualizing a molecular model and its vibration modes, further including:

[0133] Step 7: Determine the molecular vibration result according to the visual output, and perform corresponding analysis on the molecular vibration result; wherein, the molecular vibration result is: which atomic vibration mode is represented by which synthesis vector;

[0134] Wherein, Step 7: Determine the molecular vibration result according to the visual output, and perform corresponding analysis on the molecular vibration result, including:

[0135] Obtain the molecular vibration analysis requirements of the visual output; wherein, the molecular vibration analysis requirements are: what kind of vibration analysis requirements are needed for the molecular structure of the visual output, for example: analyzing the influence of chemical bonds between atoms on molecular vibration, and for another example: the influence of the interaction between molecular atoms on molecular vibration;

[0136] Analyze the molecular vibration analysis requirements to obtain multiple vibration analysis requirement items; wherein, the vibration analysis requirement item is: the specific content of the vibration analysis requirement;

[0137] Construct a data extraction template according to the vibration analysis requirement item; wherein, the data extraction template is: a template that restricts the extraction of only the analysis data required by the vibration analysis requirement item;

[0138] Based on big data, determine the first target big data according to the data extraction template;

[0139] Determine the analysis result according to the molecular vibration result and the first target big data.

[0140] The working principle and beneficial effects of the above technical solution are:

[0141] Generally, researchers study the molecular model and molecular vibration modes by consulting literature on their own to study the vibration behavior of molecules. Therefore, this application introduces the molecular vibration analysis requirements of the visual output, constructs a data extraction template according to the vibration analysis requirement items and extracts the first target big data, and determines the analysis result according to the molecular vibration result and the first target big data. This application combines visual output and big data analysis, can determine different vibration modes corresponding to multiple frequencies of molecules, and reveal and analyze the regularity of molecular vibration, which helps to understand the vibration behavior of molecules and provides a basis and direction for subsequent applications and research.

[0142] In one embodiment, determining the analysis result according to the molecular vibration result and the first target big data includes:

[0143] Extract the second frequency information from the analysis results, and at the same time, extract the third frequency information of the first target big data; wherein, the second frequency information is: the vibration mode represented by the synthetic vector corresponding to the atoms in the analysis results; the third frequency information is: the vibration modes of each atom determined based on the first target big data;

[0144] Determine the frequency distribution according to the second frequency information and the third frequency information; wherein, the frequency distribution is: a chart visualizing the atomic vibration modes and corresponding vibration frequencies within a molecule, showing the intensities of the vibrations of atoms with different vibration modes in the molecule;

[0145] Analyze the frequency distribution to determine multiple frequency interpolations; wherein, the frequency interpolation is: the overlapping part of the second frequency information and the third frequency information in the frequency distribution;

[0146] Cluster the frequency interpolations to obtain a clustering set with the target number; wherein, clustering the frequency interpolations is implemented based on the K-means clustering algorithm, and the target number is the K value of the K-means clustering algorithm, which is set manually by the user;

[0147] Determine the average frequency interpolation of each clustering set; wherein, the average frequency interpolation is the result obtained by averaging the frequency interpolations in the clustering set;

[0148] Intercept the target frequency distribution according to the average frequency interpolation and the frequency distribution; wherein, the target frequency distribution is the result obtained by intercepting the frequency distribution between the average frequency interpolations;

[0149] Obtain the second target big data according to the target frequency distribution;

[0150] Determine the analysis results according to the molecular vibration results and the second target big data;

[0151] Among them, obtaining the second target big data according to the target frequency distribution includes:

[0152] Determine the third frequency information corresponding to the target frequency distribution and use it as the fourth frequency information;

[0153] Obtain the first target big data corresponding to the fourth frequency information and use it as the second target big data.

[0154] The working principle and beneficial effects of the above technical solution are:

[0155] The present application determines the frequency distribution based on the second frequency information extracted from the analysis results and the third frequency information extracted from the first target big data, obtains the frequency interpolation corresponding to the second frequency information in the frequency distribution, clusters the frequency interpolation and calculates the average frequency interpolation of the clustering set, and intercepts the target frequency distribution based on the average frequency interpolation and the frequency distribution to obtain the second target big data corresponding to the target frequency distribution, making the selection of the frequency interval more appropriate and reducing the influence of extreme cases on the analysis results.

[0156] In one embodiment, determining the analysis result according to the molecular vibration result and the second target big data includes:

[0157] Training a vibration demonstration model according to the second target big data; wherein, the vibration demonstration model is a three-dimensional demonstration model for demonstrating molecular vibration by simulating a molecular model based on the target big data;

[0158] Obtaining the second vibration displacement demonstrated by the vibration demonstration model; wherein, the second vibration displacement is the displacement or the degree of deviation from the equilibrium position of the atoms in the molecule in the vibration demonstration model under a specific vibration mode;

[0159] Comparing the first vibration displacement and the second vibration displacement to determine whether there is a difference in rules; the differences in rules include: vibration period and vibration amplitude;

[0160] If there is a difference in rules, obtaining the demonstration model of the second vibration displacement; wherein, the demonstration model is the molecular model in the vibration demonstration model of a certain vibration frequency of a certain vibration mode with differences;

[0161] Comparing the molecular model and the demonstration model to determine the model differences; the model differences include: chemical bond parameters and field parameters; wherein, the chemical bond parameters include: bond length, bonding direction, and the included angle of basis vectors, etc.; the field parameters include: the interaction between molecules and the polar potential field that may exist in a certain direction of the molecular model;

[0162] Based on a preset analysis model, according to the chemical bond parameters and field parameters, determining the analysis result corresponding to the model differences. Wherein, the analysis model is an AI model that replaces manual analysis of the differences in vibration rules according to the differences in chemical bond parameters and field parameters between molecular models; the analysis results include: what kind of chemical parameters and what kind of field parameters will cause what kind of special molecular vibration displacement.

[0163] The working principle and beneficial effects of the above technical solution are:

[0164] This application trains a vibration demonstration model based on the obtained second target big data, compares the first vibration displacement with the second vibration displacement of the vibration demonstration model, determines the vibration law difference. When there is a law difference, a static demonstration model is determined and compared to obtain the model difference. An analysis model is introduced, and the analysis results are attributed according to the chemical bond parameters and field parameters corresponding to the model difference, improving the suitability of the analysis process.

[0165] An embodiment of the present invention provides a visualization system for a molecular model and its vibration mode, as Figure 3 shown, including:

[0166] A target calculation file acquisition subsystem 1 for acquiring a target calculation file;

[0167] A first extraction subsystem 2 for extracting the atomic positions and lattice basis vectors of target atoms in the molecular structure according to the target calculation file;

[0168] A second extraction subsystem 3 for extracting the vibration frequencies of special points in the molecular structure and the eigenvectors corresponding to each target atom according to the target calculation file;

[0169] A molecular model drawing subsystem 4 for drawing a molecular model according to the atomic positions and lattice basis vectors;

[0170] A vector synthesis subsystem 5 for extracting the real part of the eigenvector and performing vector synthesis to determine the first vibration displacement of each target atom at different vibration frequencies;

[0171] A visualization output subsystem 6 for determining the visualization output based on a preset visualization rule according to the molecular model and the first vibration displacement.

[0172] Obviously, those skilled in the art can make various changes and modifications to the present invention without departing from the spirit and scope of the present invention. Thus, if these modifications and variations of the present invention fall within the scope of the claims of the present invention and their equivalent technologies, the present invention is also intended to include these changes and modifications.

Claims

1. A visualization method for a molecular model and its vibration modes, characterized in that, it includes: Step 1: Obtain a target calculation file; Step 2: Extract the atomic positions of target atoms and lattice basis vectors in the molecular structure according to the target calculation file; Step 3: Extract the vibration frequencies of special points in the molecular structure and the eigenvectors corresponding to each target atom according to the target calculation file; Step 4: Draw a molecular model according to the atomic positions and lattice basis vectors; Step 5: Extract the real part of the eigenvector and perform vector synthesis to determine the first vibration displacement of each target atom at different vibration frequencies; Step 6: Based on preset visualization rules, determine the visualization output according to the molecular model and the first vibration displacement; Step 7: According to the visualization output, determine the molecular vibration result and perform corresponding analysis on the molecular vibration result, including: Obtain the molecular vibration analysis requirements of the visualization output; Analyze the molecular vibration analysis requirements to obtain multiple vibration analysis requirement items; Construct a data extraction template according to the vibration analysis requirement items; Based on big data, determine the first target big data according to the data extraction template; According to the molecular vibration result and the first target big data, determine the analysis result, including: Extract the second frequency information from the analysis result, and at the same time, extract the third frequency information of the first target big data; Determine the frequency distribution according to the second frequency information and the third frequency information; Analyze the frequency distribution to determine multiple frequency interpolations; Cluster the frequency interpolations to obtain a clustering set with the target number; Determine the average frequency interpolation of each clustering set; Intercept the target frequency distribution according to the average frequency interpolation and the frequency distribution; Obtain the second target big data according to the target frequency distribution; Determine the analysis result according to the molecular vibration result and the second target big data; Among them, obtaining the second target big data according to the target frequency distribution includes: Determine the third frequency information corresponding to the target frequency distribution and use it as the fourth frequency information; Obtain the first target big data corresponding to the fourth frequency information and use it as the second target big data; Among them, determining the analysis result according to the molecular vibration result and the second target big data includes: Train a vibration demonstration model according to the second target big data; Obtain the second vibration displacement demonstrated by the vibration demonstration model; Compare the first vibration displacement and the second vibration displacement to determine whether there is a difference in rules; the differences in rules include: vibration period and vibration amplitude; If there is a difference in rules, obtain the demonstration model of the second vibration displacement; Compare the molecular model and the demonstration model to determine the model difference; the model differences include: chemical bond parameters and field parameters; Based on a preset analysis model, determine the analysis result corresponding to the model difference according to the chemical bond parameters and field parameters.

2. The visualization method for a molecular model and its vibration modes according to claim 1, characterized in that, Step 1: Obtain a target calculation file, including: Obtain the data file of the first-principles calculation software; Obtain the call script of the PWphonon module; Determine the target calculation file according to the call script and the data file.

3. The visualization method for a molecular model and its vibration modes according to claim 1, characterized in that, Step 3: According to the target calculation file, extract the vibration frequencies of the special points of the molecular structure and the eigenvectors corresponding to each target atom, including: Step 3.1: Create an empty array; Step 3.2: Obtain the target pointer; Step 3.3: Search for the target array through the target pointer; Step 3.4: If the search is successful, determine the first frequency information of a specific wave vector of the target array, and store the first frequency information into the corresponding empty array; Step 3.5: If the determination of the first frequency information is successful, continue to search for the eigenvector, and store the real part and the imaginary part of the eigenvector into the corresponding empty array; Step 3.6: Loop and execute Steps 3.2 to 3.5 until the search result of the target pointer in Step 3.3 is not the target array.

4. A visualization method for a molecular model and its vibration mode as claimed in claim 1, characterized in that Step 4: Draw a molecular model according to the atomic positions and the lattice basis vectors, including: Create a three-dimensional space; Draw the lattice boundary points and the lattice frame according to the lattice basis vectors; Determine a three-dimensional crystal according to the lattice boundary points and the lattice frame; Obtain the element names of the target atoms; Construct a molecular model in the three-dimensional space according to the three-dimensional crystal and the element names.

5. A visualization method for a molecular model and its vibration mode as claimed in claim 4, characterized in that Constructing a molecular model in the three-dimensional space according to the three-dimensional crystal and the element names, including: Determine the first index keyword according to the element name; Determine the second index keyword, the atomic diameter, and the color mapping scheme according to the periodic table of elements; Perform keyword matching on the determined first index keyword and the second index keyword; If the matching is successful, use the atomic diameter corresponding to the second index keyword as the target diameter of the target atom corresponding to the first index keyword, and at the same time, use the color mapping scheme corresponding to the second index keyword as the target color mapping scheme of the target atom; Obtain the configuration template of the three-dimensional space; Based on the configuration template, determine the configuration parameters according to the target diameter and the target color mapping scheme; Configure the three-dimensional space according to the configuration parameters to obtain the molecular model constructed in the three-dimensional space.

6. A visualization method for a molecular model and its vibration mode as claimed in claim 1, characterized in that Step 6: Based on the preset visualization rules, determine the visualization output according to the molecular model and the first vibration displacement, including: Obtain the view control instructions of the target person; the view control instructions include: elevation angle control instructions and azimuth angle control instructions; According to the view control instructions, control the process output, and obtain the visualization output after the control is completed.

7. A visualization system for a molecular model and its vibration mode, characterized in that comprising: A target calculation file acquisition subsystem for acquiring a target calculation file; A first extraction subsystem for extracting the atomic positions and the lattice basis vectors of the target atoms in the molecular structure according to the target calculation file; A second extraction subsystem for extracting the vibration frequencies of the special points of the molecular structure and the eigenvectors corresponding to each target atom according to the target calculation file; A molecular model drawing subsystem for drawing a molecular model according to the atomic positions and the lattice basis vectors; A vector synthesis subsystem is used to extract the real part of the eigenvector and perform vector synthesis to determine the first vibration displacement of each target atom at different vibration frequencies; A visualization output subsystem is used to determine the visualization output based on the preset visualization rules, according to the molecular model and the first vibration displacement; The visualization system of the molecular model and its vibration mode also performs the following operations: Obtain the molecular vibration analysis requirements of the visualization output; Analyze the molecular vibration analysis requirements to obtain multiple vibration analysis requirement items; Construct a data extraction template according to the vibration analysis requirement items; Based on big data, determine the first target big data according to the data extraction template; Determine the analysis result according to the molecular vibration result and the first target big data, including: Extract the second frequency information from the analysis result, and at the same time, extract the third frequency information of the first target big data; Determine the frequency distribution according to the second frequency information and the third frequency information; Analyze the frequency distribution to determine multiple frequency interpolations; Cluster the frequency interpolations to obtain a clustering set with the target number; Determine the average frequency interpolation of each clustering set; Intercept the target frequency distribution according to the average frequency interpolation and the frequency distribution; Obtain the second target big data according to the target frequency distribution; Determine the analysis result according to the molecular vibration result and the second target big data; Among them, obtaining the second target big data according to the target frequency distribution includes: Determine the third frequency information corresponding to the target frequency distribution and use it as the fourth frequency information; Obtain the first target big data corresponding to the fourth frequency information and use it as the second target big data; Among them, determining the analysis result according to the molecular vibration result and the second target big data includes: Train a vibration demonstration model according to the second target big data; Obtain the second vibration displacement demonstrated by the vibration demonstration model; Compare the first vibration displacement and the second vibration displacement to determine whether there is a difference in law; the differences in law include: vibration period and vibration amplitude; If there is a difference in law, obtain the demonstration model of the second vibration displacement; Compare the molecular model and the demonstration model to determine the model difference; the model differences include: chemical bond parameters and field parameters; Based on the preset analysis model, determine the analysis result corresponding to the model difference according to the chemical bond parameters and the field parameters.

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